Commit ec737360 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Defaulted to zcat instead of unzip file.

parent e2f0afca
Pipeline #2698 failed with stages
in 443 minutes and 24 seconds
......@@ -61,20 +61,20 @@ def xcor(tag, paired):
'''Use spp to calculate cross-correlation stats.'''
tag_basename = os.path.basename(utils.strip_extensions(tag, ['.gz']))
uncompressed_tag_filename = tag_basename
out, err = utils.run_pipe([
'gzip -dc %s > ' % (tag)], outfile=uncompressed_tag_filename)
# Subsample tagAlign file
NREADS = 15000000
subsampled_tag_filename = \
tag_basename + ".%d.tagAlign.gz" % (NREADS/1000000)
steps = [
'grep -v "chrM" %s' % (uncompressed_tag_filename),
'shuf -n %d --random-source=%s' % (NREADS, uncompressed_tag_filename)
]
'zcat %s' % (tag),
'grep -v "chrM"',
'shuf -n %d --random-source=%s' % (NREADS, tag)]
if paired:
steps.extend([r"""awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}'"""])
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment